Hey Chrysom,
I encountered the same issue as you, wanted to use liquid oxygen and hydrogen to make rocket fuel but nothing happened in the chemical plant. I looked up to the .lua files and factorio seems to not like negatives temperatures in chemical plants.
To make everything working go to the mod folder then ../prototypes/item/fluid.lua
and edit the default temperature and the max temperature of both, liquid hydrogen and oxygen, to 20. It will now look like this :
default_temperature = 20,
max_temperature = 20,
You will have to clean your chemical plants and pipes to get the right temperature of liquids and then the chemical plant can accept those liquids.
Hope it will help, if you have any question, don't hesitate ! :)